Longitudinal tracking reveals developmental transitions in zebrafish clock gene expression

Circadian clocks coordinate physiological and behavioral rhythms by synchronizing biological processes with environmental cues. These rhythms emerge during development, but it remains unclear whether their component genes are activated by a common program or assembled through distinct regulatory pathways. To address this, we used longitudinal luciferase reporters to monitor per3 and per2 expression across zebrafish embryonic and larval development. Although both genes are canonical components of the circadian clock, they showed strikingly different developmental regulation. Two temporal frames of circadian gene expression were identified: an embryonic stage and a larval stage, each evident under different entrainment conditions. Per3 displayed early rhythmic expression in light/dark conditions, which was independent of per2 and cry1a light-entrainment regulation, but required bmal activity. Meanwhile, per2 displayed light-responsive transcription and remained largely bmal-independent. At the same time, both genes exhibited an endogenous embryonic expression that could not be explained solely by light-driven regulation, indicating that developmental inputs contribute to clock gene activation before mature larval rhythms are established. These findings demonstrate that the zebrafish circadian system is not assembled through a single synchronized onset of clock gene expression, but through gene-specific regulatory programs that shift across development.